FunGen-xQTL Data Catalog

A

• AD GWAS Summary Statistics. Summary statistics from large-scale Alzheimer’s disease GWAS used as primary trait input for fine-mapping, TWAS, and colocalization analyses in the FunGen-xQTL flagship study.
  • Lead analysts: Six datasets from four AD meta-analyses were used, encompassing clinically confirmed late-onset AD, proxy-based AD cases, and broader dementia phenotypes.
• ADGC GWAS imputation protocol. Adapted from ADGC GWAS Data QC Protocol to generate imputed genotype data for xQTL analysis in some cohorts.
  • Lead analysts: Xuanhe Chen.
• Alzheimer’s Disease GWAS Summary Data (Bellenguez). The SNP-level association testing summary statistics for Alzheimer’s disease from Bellenguez et al 2022 Nature Genetics.
  • Lead analysts: Oluwatosin Olayinka, Hao Sun and Rui Dong.
• Alzheimer’s Disease GWAS Summary Data (Jansen). The SNP-level association testing summary statistics for Alzheimer’s disease from Jansen et al 2019 Nature Genetics.
  • Lead analysts: Oluwatosin Olayinka.
• Alzheimer’s Disease GWAS Summary Data (Kunkle). The SNP-level association testing summary statistics for Alzheimer’s disease from Kunkle et al 2019 Nature Genetics.
  • Lead analysts: Oluwatosin Olayinka.
• Alzheimer’s Disease GWAS Summary Data (Wightman). The SNP-level association testing summary statistics for Alzheimer’s disease from Wightman et al 2021 Nature Genetics.
  • Lead analysts: Oluwatosin Olayinka.

F

• FunGen-xQTL protocol data. A toy data-set consisting of 49 de-identified samples from ROSMAP project, used to illustrates the computational protocols we developed for the detection and analysis of molecular QTLs (xQTLs).
  • Lead analysts: Hao Sun.

K

• Knight-ADRC study info. The Memory and Aging Project at the Charles F.
  • Lead analysts: Xuanhe.

M

• MAGENTA study info.
  • Lead analysts: Multi-Ancestry Genomics, Epigenomics, and Transcriptomics of Alzheimer’s (MAGENTA) Project: Participants include 465 individuals (AA – 113 with AD, 118 cognitively intact controls; NHW – 116 with AD, 118 controls) ascertained by the John P.
• MiGA study info. Microglia Genomic Atlas from the Netherlands Brain Bank (NBB) and the Neuropathology Brain Bank and Research CoRE at Mount Sinai Hospital.
  • Lead analysts: Travyse Edwards.

N

• Non-Hispanic White Linkage Disequilibrium Reference Panel. LD matrices calculated from whole genome sequencing data from 16571 non-Hispanic white individuals obtained from the Genome Center for Alzheimer’s Disease (GCAD).
  • Lead analysts: Oluwatosin Olayinka.

R

• ROSMAP study info. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) study: ROS is a longitudinal clinical-pathologic cohort study of aging and Alzheimer’s disease (AD) run from Rush University that enrolled individuals from religious communities for longitudinal clinical analysis and brain donation.
  • Lead analysts: Xuanhe Chen (xuanhechenxhc@163.com).

S

• STARNET. STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD).
  • Lead analysts: Travyse Edwards.

T

• The Mount Sinai Brain Bank (MSBB) study info. This cohort study generated large-scale matched multi-Omics data in AD and control brains for exploring novel molecular underpinnings of AD.
  • Lead analysts: Xuanhe.